1 CSF cellranger QC

1.1 Objective

We are going to perform a quality control (QC) analysis of the mapping results obtained by running cellranger version 7.0.0.

We will pull together all the libraries from all the CSF subprojects.

## [1] "CSF_01"
## [1] "4608"
## [1] "4839"
## [1] "5700"
## [1] "5792"
## [1] "5929"
## [1] "CSF_02"
## [1] "7921"
## [1] "7974"
## [1] "CSF_03"
## [1] "3054"
## [1] "3087"
## [1] "3887"
## [1] "8102"
## [1] "CSF_04"
## [1] "4535"
## [1] "4776"
## [1] "5959"
## [1] "CSF_05"
## [1] "4723"
## [1] "4759"
## [1] "8084"

2 Gene Expression QC

We will start by showing the three most relevant metrics (number of reads, estimated number of recovered cells, fraction of reads in cells, mean reads per cell, fraction of reads mapped to exonic reads, and median genes per cell) obtained by cellranger for each of the working libraries. This information will give us an idea of the quality of the experiment as well as the sequencing and the mapping steps.

GEX QC metrics
cellranger v 7.0.0
Subproject GemID Cells Median UMI counts per cell Median genes per cell Median reads per cell Total genes detected Number of reads
CSF_01 4608 3984 1623 858 19472 22942 266.97M
CSF_01 4839 3504 2964 1303 41738 22837 306.87M
CSF_01 5700 8989 2310 1049 16548 23935 298.90M
CSF_01 5792 7602 3659 1517 22742 25079 303.81M
CSF_01 5929 6962 3095 1319 16182 24309 261.68M
CSF_02 7921 4813 3998 1615 30334 23910 315.94M
CSF_02 7974 10498 4237 1825 31747 26802 610.99M
CSF_03 3054 9637 2641 1030 19239 24883 360.44M
CSF_03 3087 4294 5740 1968 43336 25201 305.29M
CSF_03 3887 2480 3094 1292 28178 26006 257.35M
CSF_03 8102 1264 2696 1246 65543 22785 297.91M
CSF_04 4535 3082 3103 1291 40915 21803 263.32M
CSF_04 4776 6429 2300 1017 22923 23147 280.36M
CSF_04 5959 262 4544 1841 640043 20889 417.03M
CSF_05 4723 8296 3481 1625 13540 26009 261.25M
CSF_05 4759 4827 5096 2063 48848 24088 366.55M
CSF_05 8084 1407 3833 1676 43313 21794 165.53M

2.1 Mapping QC

Next, we will check the quality of the mapping step performed by cellranger 7.0.0 across libraries. To do so, we will compare the percentage of reads mapped to the genome, and within these mapped reads, the amount of reads mapped to intergenic regions, intronic and exonic regions. We aim to obtain libraries with a high percentage of confidently mapped reads, and specially a high percentage of exonic reads, which correspond with gene expression or RNAs. The reads mapping to intergenic regions suggest contamination of ambient DNA, whereas reads mapping to intronic regions may come from pre-mRNAs or mature spliced isoforms that retain certain introns.

## [1] "Confidently_mapped_to_genome"
## [1] "Confidently_mapped_to_intergenic_regions"
## [1] "Confidently_mapped_to_intronic_regions"
## [1] "Confidently_mapped_to_exonic_regions"
## [1] "Confidently_mapped_antisense"
## [1] "Confidently_mapped_to_transcriptome"

2.2 Sequencing saturation and depth

After assessing mapped reads, it is important to test which is the sequencing saturation and depth for each library. The sequencing saturation is dependent on the library complexity and sequencing depth. The library complexity is the total number of different transcripts present in the library and it varies between the cell types/tissues, whereas the sequencing depth is the number of paired reads per cell. For this reason, we will plot the number of detected genes as a function of depth (sequenced reads). As sequencing depth increases, more genes are detected, but this function reaches a plateau, whereby more sequenced reads does not result in more detected genes; therefore, at this point we assure we sequenced until saturation. More specifically, the sequencing saturation the fraction of confidently mapped, valid cell-barcode, valid UMI reads that had a non-unique (cell-barcode, UMI, gene).

3 VDJ-T QC

We will start by showing the three most relevant metrics (number of reads, estimated number of recovered cells, fraction of reads in cells, mean reads per cell, fraction of reads mapped to any V(D)J gene, and cells with productive V-J Spanning Pair) obtained by cellranger for each of the working libraries. This information will give us an idea of the quality of the experiment as well as the sequencing and the mapping steps.

VDJ-T QC metrics
cellranger v 7.0.0
Subproject GemID Number of reads Estimated number of cells Fraction reads in cells Mean reads per cell Reads mapped to any V D J gene Cells with productive V-J spanning pair
CSF_01 4608 13071011 815 34.80 0.02M 38.45 58.65
CSF_01 4839 15751069 1912 77.62 0.01M 72.19 77.62
CSF_01 5700 14127176 5719 62.66 0.00M 51.69 64.84
CSF_01 5792 18090339 2729 43.33 0.01M 31.17 69.11
CSF_01 5929 14573775 4297 52.51 0.00M 82.88 80.78
CSF_02 7921 19365195 3254 84.28 0.01M 77.96 82.27
CSF_02 7974 23961188 5087 83.40 0.00M 83.33 81.80
CSF_03 3054 31625455 3337 68.86 0.01M 74.82 88.04
CSF_03 3087 58251934 522 41.00 0.11M 37.93 86.21
CSF_03 3887 40533185 201 10.49 0.20M 9.93 70.65
CSF_03 8102 31291833 524 44.41 0.06M 34.81 76.15
CSF_04 4535 34189156 1376 68.33 0.02M 69.88 87.06
CSF_04 4776 37064229 4605 73.36 0.01M 73.54 81.98
CSF_04 5959 39306802 41 21.01 0.96M 17.42 87.80
CSF_05 4723 41266949 5047 76.15 0.01M 88.72 87.44
CSF_05 4759 28647282 3145 69.07 0.01M 88.84 90.02
CSF_05 8084 37516235 642 76.78 0.06M 80.21 85.98

3.1 Mapping QC

Next, we will check the quality of the V(D)J mapping step performed by cellranger 7.0.0 across libraries. To do so, we will compare the percentage of reads mapped to any germline V(D)J gene segment, and within these mapped reads, the amount of reads mapped TRA and TRB germline gene segment.

3.2 V(D)J Expression

Here, we will assess the median number of UMIs assigned to a TRA/TRB contig per cell. Low values for any of the two parameters can indicate cells with extremely low TRA/TRB expression or poor cell quality, among others.

VDJ-T expression
cellranger v 7.0.0
GemID Median_TRA_UMIs_per_Cell Median_TRB_UMIs_per_Cell
4608 2 4
4839 3 7
5700 3 8
5792 3 7
5929 5 10
7921 4 10
7974 5 10
3054 5 12
3087 4 9
3887 2 6
8102 3 8
4535 4 9
4776 4 7
5959 5 6
4723 7 13
4759 6 15
8084 4 10

3.3 V(D)J Annotation

Now, we will check the V(D)J annotation for the studied samples. To better interpret the obtained results, we will consider the information given in the cellranger web summary file. We will assess the fraction of cell-associated barcodes (with at least…), that are the following ones:

  • Cells With TRA/TRB Contig: one TRA/TRB contig annotated as a full or partial V(D)J gene.

  • Cells With CDR3-annotated TRA/TRB Contig: one TRA/TRB contig where a CDR3 was detected.

  • Cells With Productive TRA/TRB Contig: one contig that spans the 5’ end of the V region to the 3’ end of the J region for TRA/TRB, has a start codon in the expected part of the V sequence, has an in-frame CDR3, and has no stop codons in the aligned V-J region.

  • Cells With Productive V-J Spanning Pair: one productive contig for each chain of the receptor pair. As well as the correspondent the number of cells with productive V-J Spanning Pair.

For all thre previous parameters, low values can indicate poor cell quality, low yield from the RT reaction, poor specificity of the V(D)J enrichment. Moreover, we will also check:

  • Paired Clonotype Diversit Effective diversity of the paired clonotypes. It is computed as the Inverse Simpson Index of the clonotype frequencies. A value of 1 indicates a minimally diverse sample - only one distinct clonotype was detected, whereas a value equal to the estimated number of cells indicates a maximally diverse sample.
V(D)J annotation
cellranger v6.0.1
GEM ID Estimated Number of Recovered Cells Productive V-J Spanning Pair Paired Clonotype Diversity Productive contig
Fraction Cells TRA TRB
4608 815 58.65 478 109.05 65.28 93.37
4839 1912 77.62 1484 457.31 80.65 96.97
5700 5719 64.84 3708 3103.42 68.86 95.98
5792 2729 69.11 1886 998.72 72.63 96.48
5929 4297 80.78 3471 648.62 83.17 97.60
7921 3254 82.27 2677 1905.78 84.97 97.30
7974 5087 81.80 4161 748.75 84.18 97.62
3054 3337 88.04 2938 767.92 88.79 99.25
3087 522 86.21 450 322.09 90.80 95.40
3887 201 70.65 142 132.46 74.13 96.52
8102 524 76.15 399 183.30 78.63 97.52
4535 1376 87.06 1198 542.20 89.24 97.82
4776 4605 81.98 3775 2231.51 84.99 96.98
5959 41 87.80 36 41.00 90.24 97.56
4723 5047 87.44 4413 1335.79 89.72 97.72
4759 3145 90.02 2831 67.64 91.45 98.57
8084 642 85.98 552 131.26 89.10 96.88

4 VDJ-B QC

We will start by showing the three most relevant metrics (number of reads, estimated number of recovered cells, fraction of reads in cells, mean reads per cell, fraction of reads mapped to any V(D)J gene, and cells with productive V-J Spanning Pair) obtained by cellranger for each of the working libraries. This information will give us an idea of the quality of the experiment as well as the sequencing and the mapping steps.

BCR-V(D)J QC metrics
cellranger v6.0.1
GEM ID Number of Reads Estimated Number of Recovered Cells Fraction of Reads in Cells Mean Reads per Cell Fraction of Reads Mapped to any VDJ gene Cells With Productive V-J Spanning Pair
4608 49.86M 307 34.2% 162416 33.4% 262
4839 13.55M 13 48.3% 1042457 47.6% 13
5700 27.21M 205 14.3% 132750 13.6% 148
5792 38.56M 131 2.2% 294369 2.4% 111
5929 13.87M 414 92.0% 33499 90.5% 387
7921 18.35M 134 16.9% 136953 16.8% 125
7974 19.85M 1852 88.1% 10717 88.5% 1311
3054 70.44M 5748 87.8% 12255 78.7% 5734
3087 38.04M 2 0.3% 19018134 0.8% 2
3887 32.16M 14 13.9% 2297290 13.1% 12
8102 50.05M 212 51.6% 236081 39.0% 180
4535 32.81M 18 54.8% 1823031 55.1% 15
4776 30.46M 55 26.8% 553844 26.2% 51
5959 35.87M 3 67.6% 11956182 67.3% 3

4.1 Mapping QC

Next, we will check the quality of the V(D)J mapping step performed by cellranger 7.0.0 across libraries. To do so, we will compare the percentage of reads mapped to any germline V(D)J gene segment, and within these mapped reads, the amount of reads mapped IGH, IGK and IGL germline gene segment.

4.2 V(D)J Expression

Here, we will assess the median number of UMIs assigned to a IGH/IGK/IGL contig per cell. Low values for any of the three parameters can indicate cells with extremely low IGH/IGK/IGL expression or poor cell quality, among others.

V(D)J expression
cellranger v6.0.1
GEM ID Median IGH UMIs per Cell Median IGK UMIs per Cell Median IGL UMIs per Cell
4608 5.0 18 6
4839 1995.0 7406 85
5700 7.0 19 13
5792 8.0 17 17
5929 2185.5 4343 5830
7921 10.5 26 30
7974 12.0 29 27
3054 35.0 21 53
3087 22.5 NA 47
3887 21.5 66 273
8102 18.5 76 8
4535 84.0 48 1175
4776 10.0 25 15
5959 10.0 4211 2

4.3 V(D)J Annotation

Now, we will check the V(D)J annotation for the studied samples. To better interpret the obtained results, we will consider the information given in the cellranger web summary file. We will assess the fraction of cell-associated barcodes (with at least…), that are the following ones:

  • Cells With IGH/IGK/IGL Contig: one IGH/IGK/IGL contig annotated as a full or partial V(D)J gene.

  • Cells With CDR3-annotated IGH/IGK/IGL Contig: one IGH/IGK/IGL contig where a CDR3 was detected.

  • Cells With Productive IGH/IGK/IGL Contig: one contig that spans the 5’ end of the V region to the 3’ end of the J region for IGH/IGK/IGL, has a start codon in the expected part of the V sequence, has an in-frame CDR3, and has no stop codons in the aligned V-J region.

  • Cells With Productive V-J Spanning Pair: one productive contig for each chain of the receptor pair. As well as the correspondent the number of cells with productive V-J Spanning Pair.

For all thre previous parameters, low values can indicate poor cell quality, low yield from the RT reaction, poor specificity of the V(D)J enrichment. Moreover, we will also check:

  • Paired Clonotype Diversit Effective diversity of the paired clonotypes. It is computed as the Inverse Simpson Index of the clonotype frequencies. A value of 1 indicates a minimally diverse sample - only one distinct clonotype was detected, whereas a value equal to the estimated number of cells indicates a maximally diverse sample.
V(D)J annotation
cellranger v6.0.1
GEM ID Productive contig Estimated Number of Recovered Cells Median_IGL_UMIs_per_Cell Productive V-J Spanning Pair Paired Clonotype Diversity
IGH IGK IGL Fraction IGK IGH Pair Fraction IGL IGH Pair Cells
4608 86.64 92.83 5.86 307 6 79.80 5.54 262 1.47
4839 100.00 61.54 38.46 13 85 61.54 38.46 13 13.00
5700 74.63 63.41 34.15 205 13 45.85 26.34 148 158.58
5792 84.73 62.60 37.40 131 17 51.15 33.59 111 112.16
5929 93.48 67.39 33.09 414 5830 63.04 30.92 387 50.95
7921 93.28 57.46 42.54 134 30 52.99 40.30 125 128.26
7974 71.71 61.02 38.50 1852 27 44.28 26.94 1311 497.09
3054 99.79 0.43 99.53 5748 53 0.38 99.37 5734 1.02
3087 100.00 0.00 100.00 2 47 0.00 100.00 2 2.00
3887 85.71 57.14 42.86 14 273 42.86 42.86 12 8.17
8102 88.21 75.00 22.17 212 8 65.09 20.28 180 4.62
4535 88.89 55.56 38.89 18 1175 44.44 38.89 15 18.00
4776 94.55 61.82 38.18 55 15 58.18 36.36 51 46.54
5959 100.00 66.67 33.33 3 2 66.67 33.33 3 3.00

5 Data overview

## [1] "Libraries metadata"
##    project subproject gem_id library_id library_name library_barcode    hashing
## 1      CSF     CSF_01   4608     276966     4608_GEX          AZ8142 not_hashed
## 2      CSF     CSF_01   4839     276967     4839_GEX          AZ8143 not_hashed
## 3      CSF     CSF_01   5929     276968     5929_GEX          AZ8144 not_hashed
## 4      CSF     CSF_01   5700     276969     5700_GEX          AZ8145 not_hashed
## 5      CSF     CSF_01   5792     276970     5792_GEX          AZ8146 not_hashed
## 6      CSF     CSF_01   4608     277405     4608_TCR          AZ8390 not_hashed
## 7      CSF     CSF_01   4839     277406     4839_TCR          AZ8391 not_hashed
## 8      CSF     CSF_01   5929     277407     5929_TCR          AZ8392 not_hashed
## 9      CSF     CSF_01   5700     277408     5700_TCR          AZ8393 not_hashed
## 10     CSF     CSF_01   5792     277409     5792_TCR          AZ8394 not_hashed
## 11     CSF     CSF_01   4839     277410     4839_BCR          AZ8396 not_hashed
## 12     CSF     CSF_01   5929     277411     5929_BCR          AZ8397 not_hashed
## 13     CSF     CSF_02   7921     277387     7921_GEX          AZ7864 not_hashed
## 14     CSF     CSF_02   7974     277388     7974_GEX          AZ7865 not_hashed
## 15     CSF     CSF_02   7921     277401     7921_TCR          AZ8125 not_hashed
## 16     CSF     CSF_02   7974     277402     7974_TCR          AZ8126 not_hashed
## 17     CSF     CSF_02   7921     277403     7921_BCR          AZ8127 not_hashed
## 18     CSF     CSF_02   7974     277404     7974_BCR          AZ8128 not_hashed
## 19     CSF     CSF_03   3087     277820     3087_GEX          AZ8561 not_hashed
## 20     CSF     CSF_03   3887     277821     3887_GEX          AZ8562 not_hashed
## 21     CSF     CSF_03   8102     277822     8102_GEX          AZ8563 not_hashed
## 22     CSF     CSF_03   3054     277823     3054_GEX          AZ8564 not_hashed
## 23     CSF     CSF_03   3087     278634     3087_TCR          AZ8597 not_hashed
## 24     CSF     CSF_03   3887     278635     3887_TCR          AZ8598 not_hashed
## 25     CSF     CSF_03   8102     278636     8102_TCR          AZ8599 not_hashed
## 26     CSF     CSF_03   3054     278637     3054_TCR          AZ8600 not_hashed
## 27     CSF     CSF_03   3887     278638     3887_BCR          AZ8602 not_hashed
## 28     CSF     CSF_03   8102     278639     8102_BCR          AZ8603 not_hashed
## 29     CSF     CSF_03   3054     278640     3054_BCR          AZ8604 not_hashed
## 30     CSF     CSF_04   5959     278641     5959_GEX          AZ8565 not_hashed
## 31     CSF     CSF_04   4776     278642     4776_GEX          AZ8566 not_hashed
## 32     CSF     CSF_04   4535     278643     4535_GEX          AZ8567 not_hashed
## 33     CSF     CSF_04   5959     278652     5959_TCR          AZ8605 not_hashed
## 34     CSF     CSF_04   4776     278653     4776_TCR          AZ8606 not_hashed
## 35     CSF     CSF_04   4535     278654     4535_TCR          AZ8607 not_hashed
## 36     CSF     CSF_04   5959     278655     5959_BCR          AZ8608 not_hashed
## 37     CSF     CSF_04   4776     278656     4776_BCR          AZ8609 not_hashed
## 38     CSF     CSF_04   4535     278657     4535_BCR          AZ8610 not_hashed
## 39     CSF     CSF_05   8084     281088     8084_GEX          AZ9840 not_hashed
## 40     CSF     CSF_05   4759     281089     4759_GEX          AZ9841 not_hashed
## 41     CSF     CSF_05   4723     281090     4723_GEX          AZ9842 not_hashed
## 42     CSF     CSF_05   8084     280490     8084_TCR          AZ9860 not_hashed
## 43     CSF     CSF_05   4759     280491     4759_TCR          AZ9861 not_hashed
## 44     CSF     CSF_05   4723     280492     4723_TCR          AZ9862 not_hashed
##     type donor_id  wet_lab
## 1   cDNA 4608_GEX 4608_GEX
## 2   cDNA 4839_GEX 4839_GEX
## 3   cDNA 5929_GEX 5929_GEX
## 4   cDNA 5700_GEX 5700_GEX
## 5   cDNA 5792_GEX 5792_GEX
## 6  VDJ-T 4608_TCR 4608_TCR
## 7  VDJ-T 4839_TCR 4839_TCR
## 8  VDJ-T 5929_TCR 5929_TCR
## 9  VDJ-T 5700_TCR 5700_TCR
## 10 VDJ-T 5792_TCR 5792_TCR
## 11 VDJ-B 4839_BCR 4839_BCR
## 12 VDJ-B 5929_BCR 5929_BCR
## 13  cDNA 7921_GEX 7921_GEX
## 14  cDNA 7974_GEX 7974_GEX
## 15 VDJ-T 7921_TCR 7921_TCR
## 16 VDJ-T 7974_TCR 7974_TCR
## 17 VDJ-B 7921_BCR 7921_BCR
## 18 VDJ-B 7974_BCR 7974_BCR
## 19  cDNA 3087_GEX 3087_GEX
## 20  cDNA 3887_GEX 3887_GEX
## 21  cDNA 8102_GEX 8102_GEX
## 22  cDNA 3054_GEX 3054_GEX
## 23 VDJ-T 3087_TCR 3087_TCR
## 24 VDJ-T 3887_TCR 3887_TCR
## 25 VDJ-T 8102_TCR 8102_TCR
## 26 VDJ-T 3054_TCR 3054_TCR
## 27 VDJ-B 3887_BCR 3887_BCR
## 28 VDJ-B 8102_BCR 8102_BCR
## 29 VDJ-B 3054_BCR 3054_BCR
## 30  cDNA 5959_GEX 5959_GEX
## 31  cDNA 4776_GEX 4776_GEX
## 32  cDNA 4535_GEX 4535_GEX
## 33 VDJ-T 5959_TCR 5959_TCR
## 34 VDJ-T 4776_TCR 4776_TCR
## 35 VDJ-T 4535_TCR 4535_TCR
## 36 VDJ-B 5959_BCR 5959_BCR
## 37 VDJ-B 4776_BCR 4776_BCR
## 38 VDJ-B 4535_BCR 4535_BCR
## 39  cDNA 8084_GEX 8084_GEX
## 40  cDNA 4759_GEX 4759_GEX
## 41  cDNA 4723_GEX 4723_GEX
## 42 VDJ-T 8084_TCR 8084_TCR
## 43 VDJ-T 4759_TCR 4759_TCR
## 44 VDJ-T 4723_TCR 4723_TCR
## [1] "GEX QC summary table"
## # A tibble: 17 x 26
##    Subproject GemID Cells Confidently_mapped_reads_in_c~1 Median_UMI_counts_pe~2
##    <chr>      <chr> <dbl>                           <dbl>                  <dbl>
##  1 CSF_01     4608   3984                            85.8                   1623
##  2 CSF_01     4839   3504                            93.3                   2964
##  3 CSF_01     5700   8989                            93.0                   2310
##  4 CSF_01     5792   7602                            91.8                   3659
##  5 CSF_01     5929   6962                            79.4                   3095
##  6 CSF_02     7921   4813                            93.8                   3998
##  7 CSF_02     7974  10498                            89.9                   4237
##  8 CSF_03     3054   9637                            91.0                   2641
##  9 CSF_03     3087   4294                            90.2                   5740
## 10 CSF_03     3887   2480                            84.8                   3094
## 11 CSF_03     8102   1264                            86.2                   2696
## 12 CSF_04     4535   3082                            90.3                   3103
## 13 CSF_04     4776   6429                            94.0                   2300
## 14 CSF_04     5959    262                            93.0                   4544
## 15 CSF_05     4723   8296                            97.2                   3481
## 16 CSF_05     4759   4827                            95.9                   5096
## 17 CSF_05     8084   1407                            88.7                   3833
## # i abbreviated names: 1: Confidently_mapped_reads_in_cells,
## #   2: Median_UMI_counts_per_cell
## # i 21 more variables: Median_genes_per_cell <dbl>,
## #   Median_reads_per_cell <dbl>, Total_genes_detected <dbl>,
## #   Number_of_reads <dbl>, Number_of_short_reads_skipped <dbl>,
## #   Q30_RNA_read <dbl>, Q30_UMI <dbl>, Q30_barcodes <dbl>,
## #   Confidently_mapped_antisense <dbl>, ...
## [1] "VDJ-T QC summary table"
## # A tibble: 17 x 23
##    Subproject GemID Cells_with_productive_TRA_contig Cells_with_productive_TRB~1
##    <chr>      <chr>                            <dbl>                       <dbl>
##  1 CSF_01     4608                              65.3                        93.4
##  2 CSF_01     4839                              80.6                        97.0
##  3 CSF_01     5700                              68.9                        96.0
##  4 CSF_01     5792                              72.6                        96.5
##  5 CSF_01     5929                              83.2                        97.6
##  6 CSF_02     7921                              85.0                        97.3
##  7 CSF_02     7974                              84.2                        97.6
##  8 CSF_03     3054                              88.8                        99.2
##  9 CSF_03     3087                              90.8                        95.4
## 10 CSF_03     3887                              74.1                        96.5
## 11 CSF_03     8102                              78.6                        97.5
## 12 CSF_04     4535                              89.2                        97.8
## 13 CSF_04     4776                              85.0                        97.0
## 14 CSF_04     5959                              90.2                        97.6
## 15 CSF_05     4723                              89.7                        97.7
## 16 CSF_05     4759                              91.4                        98.6
## 17 CSF_05     8084                              89.1                        96.9
## # i abbreviated name: 1: Cells_with_productive_TRB_contig
## # i 19 more variables:
## #   `Cells_with_productive_V-J_spanning__TRA,_TRB__pair` <dbl>,
## #   `Cells_with_productive_V-J_spanning_pair` <dbl>,
## #   Estimated_number_of_cells <dbl>, Median_TRA_UMIs_per_Cell <dbl>,
## #   Median_TRB_UMIs_per_Cell <dbl>,
## #   `Number_of_cells_with_productive_V-J_spanning_pair` <dbl>, ...
## [1] "VDJ-B QC summary table"
## # A tibble: 14 x 27
##    Subproject GemID Cells_with_productive_IGH_contig Cells_with_productive_IGK~1
##    <chr>      <chr>                            <dbl>                       <dbl>
##  1 CSF_01     4608                              86.6                       92.8 
##  2 CSF_01     4839                             100                         61.5 
##  3 CSF_01     5700                              74.6                       63.4 
##  4 CSF_01     5792                              84.7                       62.6 
##  5 CSF_01     5929                              93.5                       67.4 
##  6 CSF_02     7921                              93.3                       57.5 
##  7 CSF_02     7974                              71.7                       61.0 
##  8 CSF_03     3054                              99.8                        0.43
##  9 CSF_03     3087                             100                          0   
## 10 CSF_03     3887                              85.7                       57.1 
## 11 CSF_03     8102                              88.2                       75   
## 12 CSF_04     4535                              88.9                       55.6 
## 13 CSF_04     4776                              94.6                       61.8 
## 14 CSF_04     5959                             100                         66.7 
## # i abbreviated name: 1: Cells_with_productive_IGK_contig
## # i 23 more variables: Cells_with_productive_IGL_contig <dbl>,
## #   Cells_with_productive_V_J_spanning_IGK_IGH_pair <dbl>,
## #   Cells_with_productive_V_J_spanning_IGL_IGH_pair <dbl>,
## #   Cells_with_productive_V_J_spanning_pair <dbl>,
## #   Estimated_number_of_cells <dbl>, Median_IGH_UMIs_per_Cell <dbl>,
## #   Median_IGK_UMIs_per_Cell <dbl>, Median_IGL_UMIs_per_Cell <dbl>, ...

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